3 from django.db.models.signals import post_save, post_delete
4 from django.dispatch import receiver
5 from .models import Task
10 from string import Template
14 logger = logging.getLogger(__name__)
16 def seq_2d_xx(line,seq):
17 line=line.replace(" ","")
19 for ii in range(0,len(line)):
25 return("".join(lista))
27 def seq_2d_write(line):
28 line=line.replace(" ", "")
29 out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
31 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
32 for ii in range(1,len(line)-2):
34 if line[ii:ii+2]=='HH':
35 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
36 elif line[ii:ii+2]=='EE':
37 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
39 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
42 def seq_2d_write_50(line):
43 line=line.replace(" ", "")
44 out='{:d}\n'.format(len(line))
46 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
47 for ii in range(1,len(line)-2):
49 if line[ii:ii+2]=='HH':
50 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
51 elif line[ii:ii+2]=='EE':
52 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
54 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
57 def write_ssbond(ssbond):
60 ssbond=json.loads(ssbond)
64 list_sorted=sorted(list)
67 return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
68 str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
73 @receiver(post_save, sender=Task)
74 def write_on_task_save(sender, instance, **kwargs):
75 if instance.ready and not instance.done and instance.running==0:
76 if (not os.path.isdir(instance.jobdirname)):
77 os.mkdir(instance.jobdirname)
78 # os.chdir(instance.jobdirname)
82 #md=Template('nstep=$nstep ntwe=100 ntwx=100 dt=0.20 damax=10.0 lang=1'+
83 # 't_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
84 #wrapper = textwrap.TextWrapper(width=70)
85 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
87 if instance.unres_ff =='FF2':
88 w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
89 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
90 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
91 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 &
92 CUTOFF=7.00000 WCORR4=0.00000"""
93 elif instance.unres_ff =='NEWCT-9P':
94 w="""WSC=0.81230 WSCP=1.20420 WELEC=0.87690 WBOND=1.00000 WANG=1.97730 &
95 WSCLOC=0.063657 WTOR=1.41540 WTORD=0.00000 WCORRH=0.00000 WCORR5=0.00000 &
96 WCORR6=0.00000 WEL_LOC=0.036638 WTURN3=1.45110 WTURN4=0.00000 WTURN6=0.00000 &
97 WSCCOR=0.00000 WVDWPP=0.33393 WHPB=1.00000 WSCP14=0.00000 &
98 CUTOFF=7.00000 WCORR4=0.00000"""
100 w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 &
101 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 &
102 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 &
103 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 &
104 CUTOFF=7.00000 WCORR4=0.00000"""
107 with open(instance.jobdirname+'/file.inp','w') as f:
108 f.write(instance.name + ' UNRES server job'+ '\n')
110 if instance.type == 'min' :
112 control_line = 'SEED='+str(instance.md_seed)+' ' \
113 + instance.min_choice \
114 + ' pdbstart pdbref ' \
115 + ' BOXX='+str(instance.boxx) \
116 + ' BOXY='+str(instance.boxy) \
117 + ' BOXZ='+str(instance.boxz) +' '
118 if not instance.min_overlap:
119 control_line = control_line+'overlap '
120 if not instance.min_searchsc:
121 control_line = control_line+'nosearchsc '
122 if instance.min_pdbout:
123 control_line = control_line+'pdbout '
124 if instance.min_unres_pdb:
125 control_line = control_line+'unres_pdb '
126 if instance.unres_ff =='NEWCT-9P':
127 control_line = control_line+'tormode=2 '
129 type_line = 'print_min_ini print_min_res print_min_stat'\
130 +' MAXMIN='+str(instance.min_maxmin)\
131 +' MAXFUN='+str(instance.min_maxfun)
134 seq=instance.md_seq.replace(" ","")
142 nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
143 seq2 = ''.join([c for c in seq if c in nogly])
145 dimen3=(dimen3+len(seq2))*3
148 if instance.type == 'md' :
149 control_line = 'SEED='+str(instance.md_seed)+' '\
150 +instance.md_start +' md one_letter'\
151 + ' BOXX='+str(instance.boxx) \
152 + ' BOXY='+str(instance.boxy) \
153 + ' BOXZ='+str(instance.boxz) +' '
155 if instance.md_pdbref:
156 control_line = control_line+'pdbref '
158 if instance.unres_ff =='NEWCT-9P':
159 control_line = control_line+'tormode=2 cart'
161 type_line = ' reset_vel=0'\
162 +' t_bath='+str(instance.md_temp)\
163 +' nstep='+str(instance.md_nstep)\
164 +' ntwe='+str(instance.md_ntwe)\
165 +' ntwx='+str(instance.md_ntwx)\
166 +' dt='+str(instance.md_dt)
167 if instance.md_lang == 'langevin':
168 type_line = type_line + ' lang=1 '
169 type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
170 if instance.md_lang == 'berendsen':
171 type_line = type_line + ' lang=0 tbf '
172 type_line = type_line + 'tau_bath='+str(instance.md_tau)
173 if instance.md_respa:
174 type_line = type_line + ' respa '
175 if instance.md_mdpdb:
176 type_line = type_line + ' mdpdb '
178 if instance.type == 'remd' or instance.type == 'dock':
179 control_line = 'SEED='+str(instance.md_seed)+' '\
180 +instance.md_start +' re one_letter'\
181 + ' BOXX='+str(instance.boxx) \
182 + ' BOXY='+str(instance.boxy) \
183 + ' BOXZ='+str(instance.boxz) +' '
185 if instance.type == 'dock':
186 control_line = control_line+'CONSTR_HOMOL=24 '
188 if instance.md_pdbref:
189 control_line = control_line+'pdbref '
191 if instance.unres_ff =='NEWCT-9P':
192 control_line = control_line+'tormode=2 cart'
195 if instance.saxs_data != '':
196 lines=instance.saxs_data.split('\n')
199 if len(line.split())==2:
201 cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
202 control_line += cntrl_saxs
204 type_line = ' reset_vel='+ str(instance.remd_nstex)\
205 +' nstep='+str(instance.md_nstep)\
206 +' ntwe='+str(instance.md_ntwe)\
207 +' ntwx='+str(instance.md_ntwx)\
208 +' dt='+str(instance.md_dt)
209 if instance.md_lang == 'langevin':
210 type_line = type_line + ' lang=1 '
211 type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
212 if instance.md_lang == 'berendsen':
213 type_line = type_line + ' lang=0 tbf '
214 type_line = type_line + 'tau_bath='+str(instance.md_tau)
215 if instance.md_respa:
216 type_line = type_line + ' respa '
217 # if instance.md_mdpdb:
218 # type_line = type_line + ' mdpdb '
220 type_line2 = 'nrep='+str(instance.remd_nrep) \
221 +' nstex='+str(instance.remd_nstex) \
222 +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
223 +' traj1file rest1file TRAJCACHE=200'
225 if instance.md_start == 'pdbstart':
226 type_line = type_line + ' preminim cart'
228 wrapper = textwrap.TextWrapper(width=70)
230 word_list = wrapper.wrap(text=control_line)
231 for element in word_list[:-1]:
232 f.write('{:79}'.format(element)+'&\n')
233 f.write(word_list[-1]+'\n')
235 word_list = wrapper.wrap(text=type_line)
236 for element in word_list[:-1]:
237 f.write('{:79}'.format(element)+'&\n')
238 f.write(word_list[-1]+'\n')
240 if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P':
241 if instance.type == 'remd' or instance.type == 'dock':
242 f.write('print_min_ini print_min_res print_min_stat maxfun='+
243 str(instance.min_maxfun)+'\n')
245 f.write('print_min_ini print_min_res print_min_stat\n')
248 if instance.type == 'remd' or instance.type == 'dock':
249 word_list = wrapper.wrap(text=type_line2)
250 for element in word_list[:-1]:
251 f.write('{:79}'.format(element)+'&\n')
252 f.write(word_list[-1]+'\n')
254 tmp1=json.loads(instance.remd_multi_t)
256 word_list = wrapper.wrap(text=string1.join(tmp1))
257 for element in word_list[:-1]:
258 f.write('{:79}'.format(element)+'&\n')
259 f.write(word_list[-1]+'\n')
261 tmp1=json.loads(instance.remd_multi_m)
263 word_list = wrapper.wrap(text=string1.join(tmp1))
264 for element in word_list[:-1]:
265 f.write('{:79}'.format(element)+'&\n')
266 f.write(word_list[-1]+'\n')
268 if instance.saxs_data != '':
269 w+=' wsaxs='+str(instance.wsaxs)
273 if instance.type == 'min' or instance.md_start == 'pdbstart':
274 if instance.type == 'dock':
275 f.write('plik1ter.pdb\n')
277 f.write('plik.pdb\n')
278 f.write(write_ssbond(instance.ssbond))
279 if instance.md_2d == '':
282 if instance.unres_ff =='NEWCT-9P':
283 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
285 f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
287 if instance.type == 'dock':
288 f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
289 f.write('READ2SIGMA START_FROM_MODELS\n')
290 for i in range(1,10):
291 f.write('model0'+str(i)+'.pdb\n')
292 for i in range(10,25):
293 f.write('model'+str(i)+'.pdb\n')
295 if instance.type == 'md' and instance.md_start != 'pdbstart':
297 if instance.md_pdbref:
298 f.write('plik.pdb\n')
299 f.write(str(len(seq))+'\n')
300 for i in range(0,len(seq),80):
301 f.write(seq[i:i+80]+'\n')
303 if instance.md_2d == '':
306 if instance.unres_ff =='NEWCT-9P':
307 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
309 f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
312 if instance.type == 'remd' and instance.md_start != 'pdbstart':
314 if instance.md_pdbref:
315 f.write('plik.pdb\n')
316 f.write(str(len(seq))+'\n')
317 for i in range(0,len(seq),80):
318 f.write(seq[i:i+80]+'\n')
320 if instance.md_2d == '':
323 if instance.unres_ff =='NEWCT-9P':
324 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
326 f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
329 if instance.saxs_data != '':
330 lines=instance.saxs_data.split('\n')
334 f.write(tmp[0]+' '+tmp[1]+'\n')
337 if instance.type == 'min':
338 os.chdir(instance.jobdirname)
339 if instance.unres_ff =='FF2':
340 shutil.copy('../files/pbs.csh','.')
341 elif instance.unres_ff =='NEWCT-9P':
342 shutil.copy('../files/pbs_newct-9p.csh','pbs.csh')
344 shutil.copy('../files/pbs_new.csh','pbs.csh')
345 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
347 elif instance.type == 'md':
348 os.chdir(instance.jobdirname)
349 if instance.unres_ff =='FF2':
350 f1 = open('../files/pbs_md.csh', 'r')
351 elif instance.unres_ff =='NEWCT-9P':
352 f1 = open('../files/pbs_md_newct-9p.csh', 'r')
354 f1 = open('../files/pbs_md_new.csh', 'r')
355 f2 = open('pbs.csh', 'w')
357 f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
361 f1 = open('file.seq', 'w')
362 for i in range(0,len(seq),80):
363 f1.write(seq[i:i+80]+'\n')
367 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
370 # instance.type == 'remd'
371 tmp1=json.loads(instance.remd_multi_m)
372 nreplicas=sum(map(int, tmp1))
373 # hardcoded for 4 core nodes with FGPROC=2
374 nodes=int(nreplicas*2/4)
375 reszta = nreplicas*2-nodes*4
377 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
379 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
382 if instance.ssbond!='':
385 for i in range(0,len(seq)):
390 ss=json.loads(instance.ssbond)
392 l.append(e[0]-ix[e[0]])
393 l.append(e[1]-ix[e[1]])
394 tmp_ss=' '.join(map(str,l))
396 os.chdir(instance.jobdirname)
397 if instance.unres_ff =='FF2':
398 f1 = open('../files/pbs8.csh', 'r')
399 elif instance.unres_ff =='NEWCT-9P':
400 f1 = open('../files/pbs8_newct-9p.csh', 'r')
402 f1 = open('../files/pbs8_new.csh', 'r')
403 f2 = open('pbs8.csh', 'w')
405 if '#PBS -l nodes=4:ppn=4' in line:
406 f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
407 elif '$ssbond' in line:
408 f2.write(line.replace('$ssbond',tmp_ss))
409 elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
411 if instance.dock_peptide:
412 f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
414 f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n')
415 f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
416 f2.write("echo TER >> plik1ter.pdb \n")
417 f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")
419 tmp1=json.loads(instance.remd_multi_t)
420 f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
424 f1 = open('file.seq', 'w')
425 for i in range(0,len(seq),80):
426 f1.write(seq[i:i+80]+'\n')
432 # write wham & cluster input
433 with open(instance.jobdirname+'/file_wham.inp','w') as f:
434 if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
437 isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
438 f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
439 if instance.md_pdbref:
440 f.write('{:79}'.format('SEED='+str(instance.md_seed)+
441 ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
443 f.write('{:79}'.format('SEED='+str(instance.md_seed)+
444 ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
445 if instance.md_2d != '':
446 f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
447 if instance.type == 'dock':
448 f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
449 if instance.unres_ff =='NEWCT-9P':
450 f.write('{:79}'.format('tormode=2 ')+'&\n')
451 f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
452 ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
454 f.write('nres='+str(len(seq))+' one_letter\n')
455 for i in range(0,len(seq),80):
456 f.write(seq[i:i+80]+'\n')
458 f.write(write_ssbond(instance.ssbond))
460 if instance.type == 'dock':
461 f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
462 f.write('READ2SIGMA \n')
463 for i in range(1,10):
464 f.write('model0'+str(i)+'.pdb\n')
465 for i in range(10,25):
466 f.write('model'+str(i)+'.pdb\n')
468 if instance.md_2d != '':
469 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
471 if instance.saxs_data != '':
476 fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
477 lines=instance.saxs_data.split('\n')
481 f.write(tmp[0]+' '+tmp[1]+'\n')
482 saxs_r.append(tmp[0])
483 saxs_P.append(float(tmp[1]))
487 saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
489 for r,p in zip(saxs_r,saxs_P):
490 fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
495 f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
496 tmp1=json.loads(instance.remd_multi_t)
498 f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
499 f.write('kh= 0.0 Q0=0.0\n')
500 rec=instance.md_nstep/instance.md_ntwx
501 f.write('nfile_cx=1 rec_start='+str(rec/10)
502 +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
503 f.write('file_MD000\n')
504 if instance.md_pdbref:
506 if instance.type == 'dock':
507 f.write('plik1ter.pdb\n')
509 f.write('plik.pdb\n')
512 with open(instance.jobdirname+'/file_cluster.inp','w') as f:
513 f.write(instance.name + ' UNRES server job'+ '\n')
514 f.write('{:79}'.format('nres='+str(len(seq))
515 +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
516 +' temper='+str(instance.remd_cluter_temp))+'&\n')
517 if instance.md_2d != '':
518 f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
519 if instance.type == 'dock':
520 f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
521 if instance.unres_ff =='NEWCT-9P':
522 f.write('{:79}'.format('tormode=2 ')+'&\n')
523 f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
524 ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
526 for i in range(0,len(seq),80):
527 f.write(seq[i:i+80]+'\n')
528 f.write(write_ssbond(instance.ssbond))
529 if instance.type == 'dock':
530 f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
531 f.write('READ2SIGMA \n')
532 for i in range(1,10):
533 f.write('model0'+str(i)+'.pdb\n')
534 for i in range(10,25):
535 f.write('model'+str(i)+'.pdb\n')
536 if instance.md_2d != '':
537 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
538 if instance.saxs_data != '':
539 lines=instance.saxs_data.split('\n')
543 f.write(tmp[0]+' '+tmp[1]+'\n')
545 os.chdir(instance.jobdirname)
546 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
549 print ret_code.stdout.readlines()
550 logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
552 @receiver(post_delete, sender=Task)
553 def delete_on_task_del(sender, instance, **kwargs):
554 if instance.jobdirname:
555 if os.path.isdir(instance.jobdirname):
556 shutil.rmtree(instance.jobdirname)
557 logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)